Variant report

Variant	rs28574900
Chromosome Location	chr4:99561165-99561166
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10022548	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28591094	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28722480	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28732372	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59383241	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6532756	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991354	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594940	chr4:99542475-99573350	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28574900	RP11-1299A16.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99548000-99569200	Weak transcription	Gastric	stomach
2	chr4:99548000-99577000	Weak transcription	Esophagus	oesophagus
3	chr4:99548400-99563600	Weak transcription	HSMM	muscle
4	chr4:99549600-99563200	Weak transcription	HMEC	breast
5	chr4:99549800-99563600	Weak transcription	NHEK	skin
6	chr4:99550000-99563600	Weak transcription	HUVEC	blood vessel
7	chr4:99551800-99563200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:99552600-99569600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:99552800-99569200	Weak transcription	Fetal Stomach	stomach
10	chr4:99553200-99564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:99554000-99564000	Weak transcription	Osteobl	bone
12	chr4:99554200-99562600	Weak transcription	NH-A	brain
13	chr4:99554200-99564200	Weak transcription	Pancreas	Pancrea
14	chr4:99554200-99569200	Weak transcription	Spleen	Spleen
15	chr4:99554400-99564200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:99555000-99561600	Weak transcription	Fetal Brain Male	brain
17	chr4:99555800-99563200	Enhancers	Brain Cingulate Gyrus	brain
18	chr4:99558000-99561800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:99558000-99562000	Enhancers	Brain Substantia Nigra	brain
20	chr4:99558000-99563600	Enhancers	Brain Angular Gyrus	brain
21	chr4:99558200-99563000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr4:99558200-99564200	Weak transcription	Fetal Heart	heart
23	chr4:99558400-99563200	Weak transcription	Right Ventricle	heart
24	chr4:99559200-99561200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr4:99559400-99564400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:99559600-99563600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr4:99560200-99561200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr4:99560200-99562000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr4:99560200-99565600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:99560200-99569200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:99560400-99561200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:99560400-99561200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr4:99560400-99561600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:99560600-99561200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr4:99560600-99561200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr4:99560600-99561600	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:99560600-99562600	Weak transcription	Brain Anterior Caudate	brain
38	chr4:99560600-99564200	Weak transcription	Thymus	Thymus
39	chr4:99560600-99568000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:99560800-99561200	Active TSS	Primary T cells fromperipheralblood	blood
41	chr4:99560800-99561200	Flanking Active TSS	GM12878-XiMat	blood
42	chr4:99560800-99561200	Active TSS	NHDF-Ad	bronchial
43	chr4:99560800-99561400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:99560800-99561600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:99560800-99561600	Enhancers	Fetal Brain Female	brain
46	chr4:99560800-99562200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:99560800-99562600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:99560800-99562800	Weak transcription	Stomach Mucosa	stomach
49	chr4:99560800-99564200	Weak transcription	Fetal Thymus	thymus
50	chr4:99560800-99566400	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links